From 08672c8413b45612b4823aac89412fe037d2b1f3 Mon Sep 17 00:00:00 2001
From: Emilio Palumbo <emiliopalumbo@gmail.com>
Date: Mon, 20 Feb 2017 11:44:42 +0100
Subject: [PATCH] Fix issue with item order in mix

---
 chipseq-pipeline.nf | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/chipseq-pipeline.nf b/chipseq-pipeline.nf
index b0f8469..66eb888 100755
--- a/chipseq-pipeline.nf
+++ b/chipseq-pipeline.nf
@@ -267,8 +267,10 @@ originalBams.cross(bamsReads)
       it.value[0]
       break
     case 2:
-      def fragLen = it.value[0][1].text.split()[2].split(',')[0] as Integer
-      it.value[1][0..-4] + [fragLen] + it.value[1][-2..-1]
+      def bams = it.value.find { it[1] =~ /bam/ }
+      def paramFile = it.value.find { it[1] =~ /params/ }[1]
+      def fragLen = paramFile.text.split()[2].split(',')[0] as Integer
+      bams[0..-4] + [fragLen] + bams[-2..-1]
       break
   }
 }.tap{ allBams }